Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NIPBL

Cell type

Cell type Class
Others
Cell type
Fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
CHOPS Fibroblast
cell type
CHOPS Fibroblast
antibody
NIPBL
treatment
Non-treatment

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed as previously described (Komata, M., et al., Chromatin immunoprecipitation protocol for mammalian cells. Methods Mol Biol, 2014. 1164: p. 33-8.). Total RNA was extracted using TRIzol (Life Technologies) and Nucleospin RNA (Macherey-Nagel) following the manufacturers' instructions. ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (New England BioLabs).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
55347884
Reads aligned (%)
97.6
Duplicates removed (%)
30.6
Number of peaks
15079 (qval < 1E-05)

hg19

Number of total reads
55347884
Reads aligned (%)
91.0
Duplicates removed (%)
55.1
Number of peaks
7062 (qval < 1E-05)

Base call quality data from DBCLS SRA